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A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers.

A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers. Research Abstract Details 

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  • A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers. Abstract Text:

    shobha potluriShobha Potluri,anthony k yanAnthony K Yan,bruce r donaldBruce R Donald,chris bailey-kelloggChris Bailey-Kellogg,

    Assignment of nuclear Overhauser effect (NOE) data is a key bottleneck in structure determination by NMR. NOE assignment resolves the ambiguity as to which pair of protons generated the observed NOE peaks, and thus should be restrained in structure determination. In the case of intersubunit NOEs in symmetric homo-oligomers, the ambiguity includes both the identities of the protons within a subunit, and the identities of the subunits to which they belong. This paper develops an algorithm for simultaneous intersubunit NOE assignment and C(n) symmetric homo-oligomeric structure determinations, given the subunit structure. By using a configuration space framework, our algorithm guarantees completeness, in that it identifies structures representing, to within a user-defined similarity level, every structure consistent with the available data (ambiguous or not). However, while our approach is complete in considering all conformations and assignments, it avoids explicit enumeration of the exponential number of combinations of possible assignments. Our algorithm can draw two types of conclusions not possible under previous methods: (1) that different assignments for an NOE would lead to different structural classes, or (2) that it is not necessary to uniquely assign an NOE, since it would have little impact on structural precision. We demonstrate on two test proteins that our method reduces the average number of possible assignments per NOE by a factor of 2.6 for MinE and 4.2 for CCMP. It results in high structural precision, reducing the average variance in atomic positions by factors of 1.5 and 3.6, respectively.

    A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers. Publishing Authors By Initials

    s potluriS Potluri,ak yanAK Yan,br donaldBR Donald,c bailey-kelloggC Bailey-Kellogg,

    For similar proteins research abstracts see: proteins research

    PUBMED ID PMID:

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    A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers. Journal Published:

    PUBLICATION TYPE: Research Support, U.S. Gov't,

    Journal: Protein science : a publication of the Protein Soc

    VOLUME: 16

    Page Numbers: 69-81

    Journal Abbreviation: Protein Sci.

    ISSN: 0961-8368

    DAY: 3

    MONTH: Jan

    YEAR: 2007

    A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers. Information

    Number of References:

    LANGUAGE: eng

    NlmUniqueID: 9211750

    A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers. Keywords Mesh Terms:

    KEYWORDS: Proteins

    MESH TERMS: chemistry

    Chemical & Substance for Abstract: A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers. Information

    Substance Name: cartilage matrix protein

    Registry Number: 0

    Grant and Affiliation Information for A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers.

    AFFILIATION: Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA.

    Country: United States

    United States Research PublicationUnited States Research Publication

    AGENCY: United States NIGMS

    GRANT: R01 GM 65982

    ACRONYM: GM

    MEDLINETA: Protein Sci

    REFSOURCE:

    DATABASENAME:

    ACCESSION NUMBER:

    Number Hits: 0

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